TB-Profiler result

Run: ERR11067724
Summary

Run ID: ERR11067724

Sample name:

Date: 2024-10-05T09:17:09.318177

Number of reads: 2536056

Percentage reads mapped: 99.38

Median coverage: 77.0

Strain: lineage1.2.2.2;lineage4.8

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.84
lineage1.2.2.2 Indo-Oceanic RD239 0.85
lineage4 Euro-American None 0.16
lineage4.8 Euro-American (mainly T) RD219 0.16
lineage1 Indo-Oceanic RD239 0.84
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Gly Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Asp136Val Assoc w R - Interim
streptomycin gid c.87delC Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Asp461Asn Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Asp461Asn Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
gyrB 6620 p.Asp461Asn missense_variant 0.84 levofloxacin Assoc w R
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761110 p.Asp435Gly missense_variant 0.84 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
inhA 1673425 c.-777C>T upstream_gene_variant 0.86 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
pncA 2288835 p.Asp136Val missense_variant 0.86 pyrazinamide Assoc w R - Interim
embB 4247431 p.Met306Ile missense_variant 0.89 ethambutol Assoc w R
gid 4408115 c.87delC frameshift_variant 0.85 streptomycin Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
dnaA 371 p.Pro124Leu missense_variant 0.22 isoniazid Not assoc w R
gyrB 5075 c.-165C>T upstream_gene_variant 0.86 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.83 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.87 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.82 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.88 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.8 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.75 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.84 isoniazid Not assoc w R
Rv0010c 13548 p.Thr4Ile missense_variant 0.85 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.77 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.91 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.85 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.85 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.93 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.87 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.87 rifampicin Not assoc w R
rpoC 764154 p.Gln262Arg missense_variant 0.85 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.84 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 778992 c.-512C>T upstream_gene_variant 0.83 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.79 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254747 c.-213C>A upstream_gene_variant 0.78 levofloxacin
moxifloxacin
isoniazid
rifampicin
embR 1417019 p.Cys110Tyr missense_variant 0.73 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.75 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.8 ethambutol
atpE 1460992 c.-53A>C upstream_gene_variant 0.18 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834027 c.486G>A synonymous_variant 0.74 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.82 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.85 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918245 c.306C>T synonymous_variant 0.77 capreomycin Not assoc w R - Interim
bacA 2062922 p.Ile603Val missense_variant 0.9 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.88 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.9 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.86 pyrazinamide Uncertain significance
PPE35 2170412 c.201G>A synonymous_variant 0.11 pyrazinamide Not assoc w R - Interim
Rv1979c 2222308 p.Asp286Gly missense_variant 0.86 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.8 bedaquiline Uncertain significance
clofazimine Not assoc w R
pncA 2288982 p.Thr87Met missense_variant 0.14 pyrazinamide Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 0.84 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.84 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.79 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.87 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.8 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.86 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
alr 3840764 c.657G>C synonymous_variant 0.18 cycloserine
rpoA 3878817 c.-310T>A upstream_gene_variant 0.85 rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.84 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.84 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.78 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.87 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.82 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.82 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.8 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.77 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.87 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.88 ethionamide Uncertain significance
ethA 4326617 p.Tyr286Ala missense_variant 0.17 ethionamide
ethR 4328030 p.Ala161Gly missense_variant 0.25 ethionamide
whiB6 4338203 p.Arg107Cys missense_variant 0.88 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.89 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.84 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.87 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.74 streptomycin Not assoc w R